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Sharing data is part of Counsyl’s DNA

Team Genomic: Matthew Leggett, Chris Beaumont, Matthew Rassmussen, and David Tran
Team Genomic: Matthew Leggett, Chris Beaumont, Matthew Rassmussen, and David Tran

Every year a group of engineers and scientists at Counsyl take the genetic variants they’ve teased out after many long fluorescent-lit hours of sequencing – and share the data. The beneficiary of this hard-won information? Everyone. Or rather anyone who uses ClinVar, an open data archive set up by the National Institutes on Health to advance our understanding of the role of genetic variants in health. The more thoroughly these gene variations are known, the higher the quality of the information available to patients who want to manage their health risks.

“There’s a gestalt of sharing here at Counsyl that we’ve made a priority,” says engineer Chris Beaumont, a member of the team that most recently submitted data to ClinVar, noting the information is not patient-specific and complies with HIPAA regulations. “Here, access doesn’t just mean affordable screening for all; it also means access to information.”

“There’s a gestalt of sharing here that we’ve made a priority”

That spirit of sharing has helped define the company from its start. When Counsyl released its first DNA screen in 2009 it was customary for genetic testing companies to treat sequencing breakthroughs as proprietary information. Counsyl made a different call. It has always made its data public, including sharing findings on more than 23,000 patients screened for carrier states in Genetics in Medicine (2013). Counsyl was an early contributor to ClinVar and it participates in the Global Alliance for Genomics and Health, which aims to promote genomic medicine by standardizing information sharing.

Counsyl’s willingness to share has attracted the attention of free-the-data activists, including filmmaker Joanna Rudnick, who lobbied hard for improving access to screening after being diagnosed with a mutation in BRCA1 when she was 27 and discovering the prohibitive cost of screening. In a recent talk at Counsyl she shared the difference that publishing rather than patenting genetic information has made to people like her. “We hoped one day the test would be under $1,000,” she said. “It’s nice to be realizing that eventuality.”

“It’s troubling that the information is out there but you don’t know it”

The genomics team, which includes Matt Rasmussen, Matthew Leggett, and David Tran, is working on making its submissions more automated and frequent. The work can be tedious but the payoff is huge. For every instance that scientists have to collect information that’s not in ClinVar, several more hours of labor must be spent researching alleles. “The more we can do to get the data out there the more we can do to scale this effort so we’re not spending several hours per variant,” says Chris, who helped develop an infrastructure for data sharing while working in Harvard’s Astronomy department.

There are still companies that don’t share data on ClinVar, which explains why Joanna Rudnick and others continue to work as free the data activists. (Counsyl is featured in the Free the Data Hall of Fame.) It also means that some companies know more about the health risks associated with mutations in a given gene than others, which means some patients may not have access to this vital information. “It’s troubling that this information is out there but you as a consumer don’t know it,” says Chris. “Our goal is to identify every mutation as either benign or deleterious.” And then share it.

Submissions to ClinVar by organization

The data that Counsyl shares with ClinVar is particularly rich. Each point on the plot above shows a particular organization's contribution to ClinVar. The horizontal axis shows the total number of mutations reported to the database. The vertical axis shows how many literature references have been associated with these mutations. Compared to other organizations with a similar number of total classifications, Counsyl has recorded a larger number of literature references. Counsyl's contribution to ClinVar is both
The data that Counsyl shares with ClinVar is particularly rich. Each point on the plot above shows a particular organization’s contribution to ClinVar. The horizontal axis shows the total number of mutations reported to the database. The vertical axis shows how many literature references have been associated with these mutations. Compared to other organizations with a similar number of total classifications, Counsyl has recorded a larger number of literature references. Counsyl’s contribution to ClinVar is both “wide” and “deep” — it has classified many mutations, each of which is associated with a rich set of literature references.

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